Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(stringr)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name
## [1] "cd8"
graph_weight
## [1] "5.0"

Check enrichment of gene sets

Read in gene info and gene set assignments

file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    2.00   21.00   22.00   20.98   22.00   23.00
length(n_genes)
## [1] 40
sort(n_genes)
##  [1]  2 18 19 19 20 20 20 21 21 21 21 21 21 21 21 21 21 21 22 22 22 22 22 22 22
## [26] 22 22 22 22 22 22 22 22 22 23 23 23 23 23 23

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}
## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"
table(is.na(a2s))
## 
## FALSE  TRUE 
##  1607    42
table(a2s == assayed_genes, useNA = 'ifany')
## 
## FALSE  TRUE  <NA> 
##    42  1565    42
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]
##     sym_in_data sym_limma
##  1:    C10orf91 LINC02870
##  2:    C12orf10      MYG1
##  3:    C12orf45  NOPCHAP1
##  4:     C6orf48    SNHG32
##  5:     C6orf99 LINC02901
##  6:    CXorf40A     EOLA1
##  7:     CXorf57      RADX
##  8:     FAM102A     EEIG1
##  9:     FAM173A    ANTKMT
## 10:     FAM213B    PRXL2B
## 11:       H2AFX      H2AX
## 12:   HIST1H2AG    H2AC11
## 13:   HIST1H2BK    H2BC12
## 14:   HIST1H2BN    H2BC15
## 15:    HIST1H3A      H3C1
## 16:    HIST1H3H     H3C10
## 17:    HIST1H4C      H4C3
## 18:   HIST2H2BF    H2BC18
## 19:    KIAA0391     PRORP
## 20:        QARS     EPRS1
## 21:       SEPT6   SEPTIN6
## 22:       ARNTL     BMAL1
## 23:    C12orf65     MTRFR
## 24:    C16orf72   HAPSTR1
## 25:      CCDC84   CENATAC
## 26:      DOPEY2     DOP1B
## 27:     FAM126B     HYCC2
## 28:    FAM160B1    FHIP2A
## 29:        H1FX     H1-10
## 30:       H2AFJ      H2AJ
## 31:       HEXDC      HEXD
## 32:    HIST1H1C      H1-2
## 33:    HIST1H1D      H1-3
## 34:    HIST1H1E      H1-4
## 35:    KIAA1109     BLTP1
## 36:    KIAA1551     RESF1
## 37:        MKL1     MRTFA
## 38:       NARFL     CIAO3
## 39:       SEPT2   SEPTIN6
## 40:      TARSL2     TARS3
## 41:      TMEM8A     PGAP6
## 42:       WDR60   DYNC2I1
##     sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)
## [1] 1649    3
gene_info[1:5,]
##    sym_in_data sym_limma gene_symbol
## 1:      ABLIM1    ABLIM1      ABLIM1
## 2:  AC004687.1      <NA>  AC004687.1
## 3:  AC004854.2      <NA>  AC004854.2
## 4:  AC007384.1      <NA>  AC007384.1
## 5:  AC007952.4      <NA>  AC007952.4
t1 = table(gene_info$gene_symbol)
table(t1)
## t1
##    1    2 
## 1647    1
gene_info[gene_symbol %in% names(t1)[t1 == 2],]
##    sym_in_data sym_limma gene_symbol
## 1:       SEPT6   SEPTIN6     SEPTIN6
## 2:       SEPT2   SEPTIN6     SEPTIN6
gene_info[sym_in_data == "HIST1H2BC", gene_symbol:="H2BC4"]
gene_info[sym_in_data == "HIST1H2BG", gene_symbol:="H2BC8"]
gene_info[sym_in_data == "SEPT6", gene_symbol:="SEPTIN6"]
gene_info[sym_in_data == "SEPT2", gene_symbol:="SEPTIN2"]

Read in cell type-specific expression data

Cell type specific gene expression were downloaded from protein atlas.

ct = fread("../Annotation/rna_single_cell_type.tsv.gz")
dim(ct)
## [1] 1587110       4
ct[1:5,]
##               Gene Gene name             Cell type  nTPM
## 1: ENSG00000000003    TSPAN6            Adipocytes 149.5
## 2: ENSG00000000003    TSPAN6 Alveolar cells type 1   6.1
## 3: ENSG00000000003    TSPAN6 Alveolar cells type 2  10.5
## 4: ENSG00000000003    TSPAN6            Astrocytes  13.9
## 5: ENSG00000000003    TSPAN6               B-cells   1.5
length(unique(ct$`Cell type`))
## [1] 79
table(ct$`Cell type`)
## 
##                      Adipocytes           Alveolar cells type 1 
##                           20090                           20090 
##           Alveolar cells type 2                      Astrocytes 
##                           20090                           20090 
##                         B-cells             Basal keratinocytes 
##                           20090                           20090 
##           Basal prostatic cells         Basal respiratory cells 
##                           20090                           20090 
## Basal squamous epithelial cells                   Bipolar cells 
##                           20090                           20090 
##          Breast glandular cells      Breast myoepithelial cells 
##                           20090                           20090 
##                  Cardiomyocytes                  Cholangiocytes 
##                           20090                           20090 
##                      Club cells           Collecting duct cells 
##                           20090                           20090 
##        Cone photoreceptor cells                Cytotrophoblasts 
##                           20090                           20090 
##                 dendritic cells              Distal enterocytes 
##                           20090                           20090 
##            Distal tubular cells                    Ductal cells 
##                           20090                           20090 
##                Early spermatids      Endometrial ciliated cells 
##                           20090                           20090 
##       Endometrial stromal cells               Endothelial cells 
##                           20090                           20090 
##           Enteroendocrine cells                 Erythroid cells 
##                           20090                           20090 
##              Excitatory neurons        Exocrine glandular cells 
##                           20090                           20090 
##       Extravillous trophoblasts                     Fibroblasts 
##                           20090                           20090 
##   Gastric mucus-secreting cells     Glandular and luminal cells 
##                           20090                           20090 
##                    granulocytes                 Granulosa cells 
##                           20090                           20090 
##                     Hepatocytes                  Hofbauer cells 
##                           20090                           20090 
##                Horizontal cells              Inhibitory neurons 
##                           20090                           20090 
##         Intestinal goblet cells                       Ionocytes 
##                           20090                           20090 
##                   Kupffer cells                Langerhans cells 
##                           20090                           20090 
##                 Late spermatids                    Leydig cells 
##                           20090                           20090 
##                     Macrophages                     Melanocytes 
##                           20090                           20090 
##                Microglial cells                       monocytes 
##                           20090                           20090 
##           Mucus glandular cells               Muller glia cells 
##                           20090                           20090 
##                        NK-cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes      Pancreatic endocrine cells 
##                           20090                           20090 
##                    Paneth cells               Peritubular cells 
##                           20090                           20090 
##                    Plasma cells       Prostatic glandular cells 
##                           20090                           20090 
##            Proximal enterocytes          Proximal tubular cells 
##                           20090                           20090 
##      Respiratory ciliated cells         Rod photoreceptor cells 
##                           20090                           20090 
##             Salivary duct cells                   Schwann cells 
##                           20090                           20090 
##          Serous glandular cells                   Sertoli cells 
##                           20090                           20090 
##               Skeletal myocytes             Smooth muscle cells 
##                           20090                           20090 
##                   Spermatocytes                   Spermatogonia 
##                           20090                           20090 
##       Squamous epithelial cells        Suprabasal keratinocytes 
##                           20090                           20090 
##            Syncytiotrophoblasts                         T-cells 
##                           20090                           20090 
##                     Theca cells         Thymic epithelial cells 
##                           20090                           20090 
##          Undifferentiated cells 
##                           20090
ct_immune = fread("../Annotation/rna_immune_cell_monaco.tsv.gz")
dim(ct_immune)
## [1] 602700      5
ct_immune[1:5,]
##               Gene Gene name                Immune cell TPM pTPM
## 1: ENSG00000000003    TSPAN6                   basophil  NA  1.2
## 2: ENSG00000000003    TSPAN6  Central memory CD8 T-cell  NA  1.7
## 3: ENSG00000000003    TSPAN6         classical monocyte  NA  0.2
## 4: ENSG00000000003    TSPAN6 Effector memory CD8 T-cell  NA  0.7
## 5: ENSG00000000003    TSPAN6    Exhausted memory B-cell  NA  0.7
summary(ct_immune$TPM)
##    Mode    NA's 
## logical  602700
summary(ct_immune$pTPM)
##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
##     0.00     0.00     3.10    49.74    27.20 96572.50
summary(ct_immune$pTPM[ct_immune$pTPM > 0])
##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
##     0.10     1.70    11.60    67.96    42.80 96572.50
length(unique(ct_immune$`Immune cell`))
## [1] 30
table(ct_immune$`Immune cell`)
## 
##                            basophil           Central memory CD8 T-cell 
##                               20090                               20090 
##                  classical monocyte          Effector memory CD8 T-cell 
##                               20090                               20090 
##             Exhausted memory B-cell               intermediate monocyte 
##                               20090                               20090 
##                         MAIT T-cell               Memory CD4 T-cell TFH 
##                               20090                               20090 
##               Memory CD4 T-cell Th1          Memory CD4 T-cell Th1/Th17 
##                               20090                               20090 
##              Memory CD4 T-cell Th17               Memory CD4 T-cell Th2 
##                               20090                               20090 
##                          myeloid DC                        naive B-cell 
##                               20090                               20090 
##                    naive CD4 T-cell                    naive CD8 T-cell 
##                               20090                               20090 
##                          neutrophil                             NK-cell 
##                               20090                               20090 
##              non-classical monocyte          Non-switched memory B-cell 
##                               20090                               20090 
##                       Non-Vd2 gdTCR                         Plasmablast 
##                               20090                               20090 
##                     plasmacytoid DC                     Progenitor cell 
##                               20090                               20090 
##              Switched memory B-cell                               T-reg 
##                               20090                               20090 
## Terminal effector memory CD4 T-cell Terminal effector memory CD8 T-cell 
##                               20090                               20090 
##                          total PBMC                           Vd2 gdTCR 
##                               20090                               20090
lineage = fread("../Annotation/rna_immune_cell_monaco_cell_types.tsv")
dim(lineage)
## [1] 30  2
lineage[1:2,]
##     Cell_type      Lineage
## 1:   Basophil Granulocytes
## 2: Neutrophil Granulocytes

Check gene expression for each gene set

dim(gene_info)
## [1] 1649    3
for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]

  n_genes = sum(genes %in% ct_immune$`Gene name`)
  print(sprintf("found %d genes.", n_genes))

  if(n_genes == 0) { next }

  df = ct_immune[`Gene name` %in% genes,]
  dim(df)
  df[1:2,]
  
  stopifnot(all(str_to_lower(df$`Immune cell`) %in% 
                  str_to_lower(lineage$Cell_type)))
  
  mat1 = match(str_to_lower(df$`Immune cell`), 
               str_to_lower(lineage$Cell_type))
  
  df = cbind(df, lineage[mat1,])
  df[1:2,]
  
  df$Cell_type = factor(df$Cell_type, levels = lineage$Cell_type)
  df = df[df$Lineage != "Total PBMC",]
  df$Lineage   = factor(df$Lineage, 
                        levels = setdiff(lineage$Lineage, "Total PBMC"))
  
  p1 = ggplot(df, aes(x=Cell_type, y=log10(pTPM + 0.1), fill=Lineage)) + 
    geom_boxplot() + xlab("Cell type") + ggtitle(set_k) + 
    theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
    scale_fill_brewer(palette="RdBu")

  print(p1)
}
## [1] 1
##  [1] "CD83"   "RHOC"   "RPL41"  "TLE4"   "ASCL2"  "CD226"  "GNLY"   "MKLN1" 
##  [9] "PLAC8"  "PRR5L"  "PTPN4"  "SPN"    "THADA"  "TMSB10" "TMSB4X" "UVRAG" 
## [17] "VPS18"  "VPS39"  "XPO6"   "YPEL5"  "ZZEF1" 
## [1] "found 21 genes."

## [1] 2
##  [1] "DTHD1"   "GSTM1"   "NT5DC1"  "SLC27A5" "SLC4A4"  "TRAV8-4" "ZNF862" 
##  [8] "ADCY7"   "ARAP2"   "BICRAL"  "DIAPH2"  "DMTF1"   "GPR141"  "MCTP2"  
## [15] "MIAT"    "MTERF2"  "MYBL1"   "NFATC3"  "NLRC3"   "TUT7"    "UNC13D" 
## [22] "XIST"    "ZNF83"  
## [1] "found 21 genes."

## [1] 3
##  [1] "APMAP"     "CD84"      "CMC1"      "FAM118A"   "FCER1G"    "ICAM3"    
##  [7] "KLRF1"     "KLRG1"     "LEPROTL1"  "LETMD1"    "LRRC23"    "NCR1"     
## [13] "RTN3"      "SH2D1A"    "THAP9-AS1" "TMEM107"   "TMEM42"    "MCOLN2"   
## [19] "PATL2"     "PCSK7"     "RASA3"     "SLFN5"    
## [1] "found 21 genes."

## [1] 4
##  [1] "ARHGAP9"  "CYB5D2"   "HLA-DMB"  "INTS8"    "KLRB1"    "MZT2A"   
##  [7] "PDE3B"    "RCSD1"    "ABCC1"    "AHCTF1"   "DOPEY2"   "ENTPD4"  
## [13] "HLA-DQA1" "KLRD1"    "LPCAT1"   "PNPLA6"   "PTPN7"    "SLC38A10"
## [19] "ST6GAL1"  "TAP2"     "UGGT1"   
## [1] "found 21 genes."

## [1] 5
##  [1] "ACTR1B"   "ATP5MG"   "COQ7"     "CPNE1"    "FAM102A"  "GLRX5"   
##  [7] "MARCKSL1" "MPST"     "NMT2"     "RACK1"    "UIMC1"    "WDR86"   
## [13] "DNAJB14"  "GDPD5"    "HERC3"    "HERC6"    "KIAA0232" "NUP210"  
## [19] "R3HCC1L"  "ZNF335"   "ZNF800"  
## [1] "found 20 genes."

## [1] 6
##  [1] "AC245297.3"  "AL139246.5"  "BBS9"        "CRTAM"       "CXorf57"    
##  [6] "EOMES"       "HIST1H3H"    "MFNG"        "NUAK2"       "PITPNC1"    
## [11] "TRAV12-2"    "TRAV38-2DV8" "TRBV3-1"     "TRBV6-2"     "TRBV6-5"    
## [16] "CYTOR"       "FAM126B"     "GK5"         "GPR174"      "NRDC"       
## [21] "OGA"         "PARP15"      "PIK3R5"     
## [1] "found 19 genes."

## [1] 7
##  [1] "NUCB2"    "PAIP2"    "PDLIM1"   "PTGER4"   "RPL22L1"  "STMN3"   
##  [7] "CWC25"    "DENND4C"  "GIGYF1"   "GPANK1"   "HELZ"     "KIF13B"  
## [13] "L3HYPDH"  "MAN2C1"   "RNMT"     "SCAF8"    "SECISBP2" "TIMP1"   
## [19] "ZCCHC2"  
## [1] "found 19 genes."

## [1] 8
##  [1] "C10orf91" "ANKRD36B" "ANKRD36C" "C16orf72" "CD46"     "CHD9"    
##  [7] "CROCC"    "DGKD"     "EML4"     "MIGA1"    "RNF19A"   "RPS6KA5" 
## [13] "RSAD2"    "RUBCN"    "STAT4"    "STK10"    "SYNE1"    "UBE2H"   
## [19] "UBR2"     "VPS13C"   "ZNF493"   "ZNF708"  
## [1] "found 20 genes."

## [1] 9
##  [1] "ALOX5AP" "HDHD3"   "KLRK1"   "MATK"    "TMEM134" "ANKRD12" "BTBD9"  
##  [8] "CST7"    "GZMA"    "GZMB"    "IRF9"    "KLF3"    "LILRB1"  "MYO1F"  
## [15] "NKG7"    "RNF125"  "SPON2"   "SRGN"    "TMEM181" "UCP2"    "ZFAND3" 
## [1] "found 21 genes."

## [1] 10
##  [1] "AC008555.5" "AC044849.1" "AC083798.2" "AL135791.1" "COQ8A"     
##  [6] "FAM213B"    "HIKESHI"    "MTRNR2L8"   "NBPF14"     "PCMTD2"    
## [11] "PRAG1"      "RGL4"       "TOX"        "TRAV13-1"   "TRAV14DV4" 
## [16] "TRAV5"      "TRBV7-2"    "TRBV7-9"    "TRGV5"      "TRGV7"     
## [21] "WARS2"      "ZNF749"    
## [1] "found 17 genes."

## [1] 12
##  [1] "BTG1"     "HIST1H4C" "ID2"      "JADE1"    "LDLRAP1"  "MSC"     
##  [7] "PNRC1"    "WDR54"    "ZNF575"   "ARRDC3"   "BRPF1"    "COX19"   
## [13] "GCN1"     "GON4L"    "KAT6B"    "MAPK8IP3" "PHF14"    "PKD1"    
## [19] "RORA"     "USP16"    "ZNF292"  
## [1] "found 21 genes."

## [1] 13
##  [1] "AC004687.1" "AC004854.2" "AC015982.1" "AC020911.2" "AC083880.1"
##  [6] "AC091271.1" "AC103591.3" "AF213884.3" "AL357060.1" "AL451085.1"
## [11] "AL627171.1" "ARF4-AS1"   "ATP2B1-AS1" "C6orf99"    "HELQ"      
## [16] "HIPK1-AS1"  "KCNQ1OT1"   "LINC01465"  "MZF1-AS1"   "OSER1-DT"  
## [21] "PGGHG"      "NEK9"      
## [1] "found 3 genes."

## [1] 14
##  [1] "AOAH"      "CCL4L2"    "TRAV3"     "TRG-AS1"   "TRGV8"     "TRGV9"    
##  [7] "CARD11"    "CARD16"    "EPSTI1"    "FCRL6"     "FGL2"      "ITM2A"    
## [13] "LINC02384" "NECAP1"    "PTPRJ"     "TRAV9-2"   "TRDC"      "TRDV1"    
## [19] "TRGC2"     "TRGV4"     "TTC38"     "XCL2"     
## [1] "found 19 genes."

## [1] 15
##  [1] "ASAH1"    "COMMD6"   "COTL1"    "ITGB1BP1" "LAPTM5"   "NSUN6"   
##  [7] "PTPRCAP"  "TPGS2"    "CCNH"     "CD2"      "CD52"     "CD8A"    
## [13] "CD8B"     "ITK"      "LY6E"     "PRSS23"   "RHOH"     "SBK1"    
## [19] "SLC35F5"  "TRAC"     "TRBC2"    "ZDHHC20" 
## [1] "found 22 genes."

## [1] 16
##  [1] "TPRKB"   "BDP1"    "CHD1"    "DHX29"   "HELZ2"   "HEXDC"   "IFI44"  
##  [8] "IFIT2"   "IFIT3"   "KLHDC4"  "MSI2"    "MX1"     "NEMF"    "OAS3"   
## [15] "PHACTR4" "PLA2G6"  "REXO1"   "RNF157"  "RNPC3"   "SPOCK2"  "VAV3"   
## [22] "ZC3H7B" 
## [1] "found 22 genes."

## [1] 17
##  [1] "IL6R"       "SERINC5"    "TRBV6-1"    "ABCA5"      "ABR"       
##  [6] "AC020659.1" "CCDC84"     "CPPED1"     "DDX3Y"      "EIF1AY"    
## [11] "ENOSF1"     "IL6ST"      "KDM5D"      "MICAL2"     "OSM"       
## [16] "RPS4Y1"     "SBNO2"      "SIDT1"      "TRBV4-2"    "ZMIZ2"     
## [21] "ZNF236"     "ZNF652"    
## [1] "found 21 genes."

## [1] 18
##  [1] "ARHGAP45"    "CEMIP2"      "CRYBG1"      "FAM133B"     "MX2"        
##  [6] "OAS2"        "PIK3CD"      "PPP4R3B"     "PREX1"       "PUM3"       
## [11] "RIPOR2"      "S100A12"     "SAMD9L"      "TENT5C"      "THUMPD3-AS1"
## [16] "TMEM131L"    "TRANK1"      "TRAV19"      "TRAV27"      "TRBV11-2"   
## [21] "TRBV2"       "TUT4"       
## [1] "found 20 genes."

## [1] 19
##  [1] "AMD1"     "CD27"     "CREBL2"   "CYB561A3" "EI24"     "GIMAP1"  
##  [7] "GLTP"     "IER3"     "IFRD1"    "KIR3DL2"  "LIME1"    "MZF1"    
## [13] "NELL2"    "PDE7A"    "PPP1R15B" "SLC38A1"  "TMEM204"  "TSPYL4"  
## [19] "LTBP4"    "TRIM38"   "VPS13A"   "ZBTB40"  
## [1] "found 22 genes."

## [1] 20
##  [1] "RGCC"     "ACOX1"    "BTN3A1"   "CAST"     "CCDC88C"  "CELF2"   
##  [7] "DDHD1"    "KDM5A"    "MTMR6"    "NCKAP1L"  "NLRC5"    "PCYT1A"  
## [13] "PRKCH"    "RAP1GAP2" "RASGRP1"  "SPG11"    "SYNRG"    "TAOK1"   
## [19] "TAOK3"    "TIPARP"   "ZEB2"    
## [1] "found 21 genes."

## [1] 21
##  [1] "ID1"        "RGS1"       "AC092683.1" "AP005482.1" "ATAD2B"    
##  [6] "BMT2"       "DOCK10"     "ETFDH"      "FAM78A"     "GABPB2"    
## [11] "GRK2"       "HRH2"       "IGKV3-15"   "LINC02256"  "MARF1"     
## [16] "MINDY2"     "NBEAL2"     "POLR2J3-1"  "SEC14L1"    "THAP5"     
## [21] "Z93930.2"   "ZNF808"    
## [1] "found 17 genes."

## [1] 22
##  [1] "ARL4A"    "ABCA7"    "CAPNS1"   "ELMO1"    "ERICH1"   "FAM53B"  
##  [7] "FNBP1"    "HSH2D"    "IFI44L"   "IL2RG"    "IRAK4"    "KCNAB2"  
## [13] "KIAA1551" "KIAA2026" "KLF6"     "PNPLA8"   "PRDM2"    "SENP7"   
## [19] "TTC14"    "WASL"     "XAF1"    
## [1] "found 21 genes."

## [1] 23
##  [1] "AC012645.3" "AC027644.3" "AC087623.3" "AK5"        "AL118516.1"
##  [6] "BX284668.6" "CHRM3-AS2"  "FXYD7"      "IGLV1-44"   "INTS6L"    
## [11] "KMT2E-AS1"  "LINC00402"  "LINC00649"  "LST1"       "MAP3K2"    
## [16] "MATR3-1"    "PDCD4-AS1"  "RETREG1"    "SNHG15"     "TRAV21"    
## [21] "TRAV8-2"    "TRAV8-3"   
## [1] "found 10 genes."

## [1] 24
##  [1] "C12orf45" "CAMK4"    "CRLF3"    "GCH1"     "PLK2"     "ZNF10"   
##  [7] "ANKRD44"  "EHMT1"    "FRYL"     "MBD5"     "PIGF"     "POLH"    
## [13] "PPP6R2"   "PRR14L"   "RLF"      "SETD2"    "SETX"     "SP3"     
## [19] "USP34"    "WDR7"     "ZNF407"  
## [1] "found 20 genes."

## [1] 25
##  [1] "AL136454.1" "ATP5F1A"    "CCNI"       "COA1"       "EFCAB2"    
##  [6] "FAM173A"    "FCMR"       "FCRL3"      "GCSAM"      "GTF3A"     
## [11] "ITGAE"      "RTRAF"      "TRBC1"      "ADGRE5"     "ARHGAP30"  
## [16] "CD38"       "CTSW"       "IFITM2"     "MT2A"       "MYO1G"     
## [21] "SLA2"       "ZNF683"    
## [1] "found 21 genes."

## [1] 26
##  [1] "AIF1"     "CD28"     "YPEL3"    "ANKRD49"  "CASP10"   "CFLAR"   
##  [7] "ETNK1"    "FNDC3B"   "GCA"      "GPATCH2L" "H6PD"     "IGHA1"   
## [13] "LSS"      "NCOA7"    "PHF11"    "PRKX"     "PTGDS"    "SETD5"   
## [19] "WDTC1"   
## [1] "found 19 genes."

## [1] 27
##  [1] "GNAQ"       "NXT2"       "AC016831.7" "ADHFE1"     "AKNA"      
##  [6] "APOL6"      "ARL4C"      "ELMOD3"     "GBP1"       "GBP5"      
## [11] "GNPTAB"     "GPR132"     "IFI27"      "INPP4A"     "ISG20"     
## [16] "PDZD4"      "PPP1R16B"   "RAB27B"     "SLFN12L"    "SYTL3"     
## [21] "TTC16"     
## [1] "found 20 genes."

## [1] 28
##  [1] "BTG2"     "C12orf10" "C12orf57" "CCNL1"    "GSTM4"    "KCTD7"   
##  [7] "MAP3K8"   "MAPRE2"   "NELFCD"   "NEU1"     "PTRHD1"   "RPS26"   
## [13] "RSRP1"    "SEPT6"    "SMDT1"    "TGIF1"    "ZFP36L1"  "ACAP3"   
## [19] "PARP4"    "TEP1"    
## [1] "found 20 genes."

## [1] 29
##  [1] "AC016405.3" "AC087239.1" "AC245014.3" "ANXA2R"     "CITED2"    
##  [6] "CSKMT"      "CXorf40A"   "IER5"       "IGKV3-20"   "ILF3-DT"   
## [11] "NOCT"       "PIK3IP1"    "SDR42E2"    "SLC2A3"     "SLC38A2"   
## [16] "STK17A"     "TC2N"       "TRBV28"     "WSB1"       "Z93241.1"  
## [21] "ZFAS1"      "MALAT1"    
## [1] "found 15 genes."

## [1] 30
##  [1] "BACH2"  "CSRNP1" "EGR1"   "EPS8"   "FOSB"   "MYLIP"  "NOSIP"  "NR1D1" 
##  [9] "NR4A2"  "NR4A3"  "RCAN3"  "SELL"   "SNHG12" "TCF7"   "TXK"    "CYTH1" 
## [17] "DUS1L"  "JUND"   "MIDN"   "SCRN3"  "VCAN"  
## [1] "found 20 genes."

## [1] 31
##  [1] "ASL"     "CLDND1"  "CXXC5"   "GATA3"   "PAPSS1"  "RAB33B"  "SESN1"  
##  [8] "SESN2"   "TBCCD1"  "TIGIT"   "CSNK1G2" "ERAP2"   "GALNT3"  "ITGAM"  
## [15] "KIR2DL3" "PYROXD1" "RAPGEF1" "RUFY2"   "SZT2"    "TBX21"   "VPS13B" 
## [22] "YPEL1"   "ZDHHC5" 
## [1] "found 23 genes."

## [1] 32
##  [1] "NT5E"    "TBC1D17" "AFF1"    "AFF4"    "ARHGAP4" "BAZ2A"   "CEP164" 
##  [8] "CRNKL1"  "LRRFIP1" "LUC7L3"  "NKTR"    "PNN"     "PPIG"    "PPIL2"  
## [15] "SRSF10"  "SRSF11"  "WDR60"   "YTHDC1" 
## [1] "found 18 genes."

## [1] 33
##  [1] "ZC3H12A" "B4GALT1" "BCL9L"   "C2CD3"   "CAPN15"  "EHBP1L1" "LONP2"  
##  [8] "LPIN1"   "NAA25"   "NFKBIZ"  "PDE4B"   "PDE4D"   "PIM1"    "RALGAPB"
## [15] "RIC3"    "STK17B"  "TBC1D2B" "TOB1"    "UTY"     "ZBTB20" 
## [1] "found 20 genes."

## [1] 34
##  [1] "GALNT11"  "ADGRG1"   "ARHGAP10" "CCL4"     "CES1"     "CX3CR1"  
##  [7] "ERBIN"    "FGFBP2"   "GALNT10"  "GALNT2"   "ITGAL"    "LAG3"    
## [13] "MPPE1"    "MYO9B"    "PEX1"     "PEX26"    "PLEK"     "SEMA4D"  
## [19] "ST8SIA4"  "SUSD1"    "TMEM8A"  
## [1] "found 21 genes."

## [1] 35
##  [1] "HMBOX1"  "KIF9"    "ANKRD36" "AP3B1"   "AP3M2"   "ARAP1"   "ARID5B" 
##  [8] "ATG2A"   "ATG2B"   "CLEC16A" "CREBZF"  "FAM13B"  "GPRIN3"  "HECTD4" 
## [15] "INO80"   "INO80D"  "INPP5D"  "KLF2"    "MKL1"    "NARFL"   "NFE2L1" 
## [22] "PIP4K2B" "ZNF557" 
## [1] "found 23 genes."

## [1] 36
##  [1] "AC025164.1" "AL121944.1" "AL138963.3" "ARMH1"      "C6orf48"   
##  [6] "CCR7"       "INPP4B"     "JAML"       "LINC02273"  "LRRN3"     
## [11] "LTB"        "NPIPB4"     "NUP58"      "TCEA3"      "TMIGD2"    
## [16] "TNFRSF25"   "TRABD2A"    "TRAV1-2"    "TRBV9"      "OXNAD1"    
## [21] "PARP11"     "PCED1B"    
## [1] "found 17 genes."

## [1] 37
##  [1] "AC007952.4"   "AC119396.1"   "ALKBH7"       "BNIP3L"       "CD40LG"      
##  [6] "CMTM7"        "DYRK4"        "EPB41L4A-AS1" "EPHX2"        "GADD45B"     
## [11] "GZMK"         "HIBADH"       "MCUB"         "NOP53"        "RGS10"       
## [16] "SNHG8"        "TCP11L2"      "TESPA1"       "TRBV20-1"     "ZFAND1"      
## [21] "ITPR2"        "LINC02446"   
## [1] "found 17 genes."

## [1] 38
##  [1] "CST3"     "MAN2B1"   "SAE1"     "TRAT1"    "ATP2B4"   "CCDC112" 
##  [7] "CMKLR1"   "CTSC"     "DOCK11"   "FAM169A"  "LNPEP"    "LRRC8A"  
## [13] "PARP14"   "RAB3GAP2" "SLC4A7"   "SLK"      "TMEM127"  "TTC17"   
## [19] "VPS13D"   "ZNF276"  
## [1] "found 20 genes."

## [1] 39
##  [1] "ABCC10"     "ARHGEF3"    "COL6A2"     "COL6A3"     "DDX60L"    
##  [6] "DENND4B"    "EIF4E3"     "HECA"       "HPS4"       "LAIR2"     
## [11] "N4BP1"      "NUTM2B-AS1" "ODF3B"      "SUSD6"      "TRAV12-3"  
## [16] "TRAV17"     "TRAV4"      "TRBV7-6"    "TRGV10"     "TSPAN32"   
## [21] "TTTY15"     "XCL1"       "ZBP1"      
## [1] "found 21 genes."

## [1] 40
##  [1] "AC007384.1"  "AC025171.3"  "ARRDC2"      "NT5C3B"      "PRR7"       
##  [6] "SNHG9"       "AC116407.2"  "ARHGEF9"     "BROX"        "CHD6"       
## [11] "DDIT4"       "GPHN"        "HIPK1"       "IQCG"        "KIAA1109"   
## [16] "PCNX1"       "PSMA3-AS1"   "SLC16A1-AS1" "SLCO3A1"     "SLF2"       
## [21] "SPATA13"     "TARSL2"      "VTI1A"      
## [1] "found 16 genes."

Session information

gc()
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  4184842 223.5   11673970 623.5         NA 11673970 623.5
## Vcells 20583330 157.1   61723001 471.0      65536 61693859 470.7
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] stringr_1.5.0     limma_3.54.2      tidyr_1.3.0       ggpubr_0.6.0     
## [5] ggplot2_3.4.2     data.table_1.14.8
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.10            png_0.1-8              Biostrings_2.66.0     
##  [4] digest_0.6.31          utf8_1.2.3             R6_2.5.1              
##  [7] GenomeInfoDb_1.34.9    backports_1.4.1        stats4_4.2.3          
## [10] RSQLite_2.3.1          evaluate_0.20          httr_1.4.6            
## [13] pillar_1.9.0           zlibbioc_1.44.0        rlang_1.1.0           
## [16] rstudioapi_0.14        car_3.1-2              jquerylib_0.1.4       
## [19] blob_1.2.4             R.oo_1.25.0            R.utils_2.12.2        
## [22] S4Vectors_0.36.2       rmarkdown_2.21         labeling_0.4.2        
## [25] RCurl_1.98-1.12        bit_4.0.5              munsell_0.5.0         
## [28] broom_1.0.4            compiler_4.2.3         xfun_0.39             
## [31] pkgconfig_2.0.3        BiocGenerics_0.44.0    htmltools_0.5.5       
## [34] tidyselect_1.2.0       KEGGREST_1.38.0        GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1           IRanges_2.32.0         fansi_1.0.4           
## [40] crayon_1.5.2           dplyr_1.1.2            withr_2.5.0           
## [43] R.methodsS3_1.8.2      bitops_1.0-7           grid_4.2.3            
## [46] jsonlite_1.8.4         gtable_0.3.3           lifecycle_1.0.3       
## [49] DBI_1.1.3              magrittr_2.0.3         scales_1.2.1          
## [52] cli_3.6.1              stringi_1.7.12         cachem_1.0.7          
## [55] carData_3.0-5          farver_2.1.1           XVector_0.38.0        
## [58] ggsignif_0.6.4         bslib_0.4.2            generics_0.1.3        
## [61] vctrs_0.6.2            RColorBrewer_1.1-3     org.Hs.eg.db_3.16.0   
## [64] tools_4.2.3            bit64_4.0.5            Biobase_2.58.0        
## [67] glue_1.6.2             purrr_1.0.1            abind_1.4-5           
## [70] fastmap_1.1.1          yaml_2.3.7             AnnotationDbi_1.60.2  
## [73] colorspace_2.1-0       rstatix_0.7.2          memoise_2.0.1         
## [76] knitr_1.44             sass_0.4.5